[English] 日本語
Yorodumi
- PDB-8yau: Crystal structure of glucose 1-dehydrogenase mutant2 from Limosil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yau
TitleCrystal structure of glucose 1-dehydrogenase mutant2 from Limosilactobacillus fermentum
ComponentsSDR family oxidoreductase
KeywordsHYDROLASE / glucose 1-dehydrogenase
Function / homologyPKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / SDR family oxidoreductase
Function and homology information
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsCong, L. / Wei, H.L. / Liu, W.D. / You, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Adv.Synth.Catal. / Year: 2024
Title: Structure-Guided Engineering of a Short-Chain Dehydrogenase LfSDR1 for Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)adenine, the Key Intermediate of Tenofovir
Authors: Wang, Q. / Cong, L. / Guo, J. / Wang, J. / Han, X. / Zhang, W. / Liu, W. / Wei, H. / You, S.
History
DepositionFeb 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase
E: SDR family oxidoreductase
F: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)158,0226
Polymers158,0226
Non-polymers00
Water4,035224
1
A: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)105,3484
Polymers105,3484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-81 kcal/mol
Surface area33840 Å2
MethodPISA
2
E: SDR family oxidoreductase

E: SDR family oxidoreductase

F: SDR family oxidoreductase

F: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)105,3484
Polymers105,3484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation7_655-x+3/2,y+1/2,-z+1/21
Buried area11830 Å2
ΔGint-94 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.749, 139.523, 331.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11F-306-

HOH

-
Components

#1: Protein
SDR family oxidoreductase


Mass: 26336.955 Da / Num. of mol.: 6 / Mutation: G92V/G146D/V186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Gene: GC247_10055
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A843R2C6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT pH 6.0, 25% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 71146 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.999 / Net I/σ(I): 19.3
Reflection shellResolution: 2.22→2.34 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 10230 / CC1/2: 0.739

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→32.56 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 3552 5 %
Rwork0.2378 --
obs0.2395 71032 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→32.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10422 0 0 224 10646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811008
X-RAY DIFFRACTIONf_angle_d1.57114858
X-RAY DIFFRACTIONf_dihedral_angle_d13.1291521
X-RAY DIFFRACTIONf_chiral_restr0.0691680
X-RAY DIFFRACTIONf_plane_restr0.0241937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.30.36213500.31596647X-RAY DIFFRACTION100
2.3-2.390.3483520.29346682X-RAY DIFFRACTION100
2.39-2.50.34013490.28986642X-RAY DIFFRACTION100
2.5-2.630.31913550.28566733X-RAY DIFFRACTION100
2.63-2.80.34893510.29096673X-RAY DIFFRACTION100
2.8-3.020.32743530.29056700X-RAY DIFFRACTION100
3.02-3.320.2783560.26116773X-RAY DIFFRACTION100
3.32-3.80.28143550.23416754X-RAY DIFFRACTION100
3.8-4.780.24393600.21326831X-RAY DIFFRACTION100
4.78-32.560.22713710.20237045X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more